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firstly I would suggest you take a look at the Procurement Implementation Manual for guidelines. It is also important wich version of E-business Suite you are on since R12 is fundamentally different than 11i10 with respect to especially the catalog management.
But at a high level you need to look at the following topics:
User/responsibility setups. Decide whether you are going to use all available functions e.g. desktop receiving, non catalog requests, punchout and services procurement.
Catalog setup/loads/structures/security. Are you going to use both internal items and bulkloaded content. How are you getting the content?
Is Automatic Document Creation already in place or should it be implemented.
Do you need to adjust the approval setup in case additional users are to use the system.
Do you need to look at account generation due to new aspects of procurement e.g. expense purchases.